Plotting range/type of discordance in alignment data

Question

[rbronste]

I was wondering if there was a way, in a Bowtie2 output, to plot the range and type of discordance? The really obvious kind when two mates are on separate chromosomes, and more subtle types such as orientation and spacing specific discordance. Just trying to tease apart the unaligned and discordant components of a bowtie2 output that looks like this:

bowtie2 --threads 12 --local --dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33

    44265166 reads; of these:
      44265166 (100.00%) were paired; of these:
        41288778 (93.28%) aligned concordantly 0 times
        1643972 (3.71%) aligned concordantly exactly 1 time
        1332416 (3.01%) aligned concordantly >1 times
    6.72% overall alignment rate

Thanks.

[h.mon]

You can try to set one of those:

--met-file <path>  send metrics to file at <path> (off)
--met-stderr       send metrics to stderr (off)

I never used them, and I don't know what kind of information they would contain.

As you used the flags --no-mixed --no-discordant, you can't get this information from the sam / bam file, which would be another possibility.